A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
eDentity Pipeline Summary
Summary statistics from the eDentity metabarcoding pipeline.
| Sample | Read Pairs | Merged (%) | Reads after trimming | After Filtering | After Derep | After Denoising | ESVs |
|---|---|---|---|---|---|---|---|
| NC1 | 22 | 100.0 | 22 | 21 | 18 | 0 | 0 |
| Sample1 | 533823 | 99.3 | 529890 | 528477 | 27705 | 2442 | 93 |
fastp
0.24.0
All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560
Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.Filtered Reads
Filtering statistics of sampled reads.
Insert Sizes
Insert size estimation of sampled reads.
Sequence Quality
Average sequencing quality over each base of all reads.
GC Content
Average GC content over each base of all reads.
N content
Average N content over each base of all reads.
Cutadapt
4.9
Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.URL: https://cutadapt.readthedocs.ioDOI: 10.14806/ej.17.1.200
Filtered Reads
This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.
Trimmed Sequence Lengths (5')
This plot shows the number of reads with certain lengths of adapter trimmed for the 5' end.
Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.
See the cutadapt documentation for more information on how these numbers are generated.
Trimmed Sequence Lengths (3')
This plot shows the number of reads with certain lengths of adapter trimmed for the 3' end.
Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.
See the cutadapt documentation for more information on how these numbers are generated.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Software | Version |
|---|---|
| Cutadapt | 4.9 |
| fastp | 0.24.0 |
